Package index • ruminate

Running ruminate

ruminate(): ruminate: Shiny app and module to facilitate pharamacometrics analysis

Helper functions

ruminate_check(): Checks ruminate Dependencies

CTS Module functions

CTS_Server(): Clinical Trial Simulator State Server

CTS_add_covariate(): Add Covariate to Elemetnt

CTS_add_rule(): Add Rule to Element

CTS_append_report(): Append Report Elements

CTS_change_source_model(): Change the Source Model

CTS_del_current_element(): Deletes Current cohort

CTS_fetch_code(): Fetch Module Code

CTS_fetch_current_element(): Fetches Current cohort

CTS_fetch_ds(): Fetch Clinical Trial Simulator Module Datasets

CTS_fetch_sc_meta(): Fetches Simulation Parameter Meta Information

CTS_fetch_state(): Fetch Clinical Trial Simulator State

CTS_init_element_model(): Initializes Cohort When Model Changes

CTS_init_state(): Initialize CTS Module State

CTS_mk_preload(): Make List of Current CTS State

CTS_new_element(): New Clinical Trial Simulation Cohort

CTS_plot_element(): Plots the Specified Element

CTS_preload(): Preload Data for CTS Module

CTS_set_current_element(): Sets the Value for the Current cohort

CTS_sim_isgood(): Checks Simulation in Element for Goodness

CTS_simulate_element(): Simulates the Specified Element

CTS_test_mksession(): Populate Session Data for Module Testing

CTS_update_checksum(): Updates CTS Module Checksum

fetch_rxinfo(): Fetches Information from an rxode2 Object

fetch_rxtc(): Extracts Timecourse and Merges Covariates

mk_subjects(): Fetches Information from an rxode2 Object

plot_sr_ev(): Plots Timecourse of Rules Simulations

plot_sr_tc(): Plots Timecourse of Rules Simulations

rx2other(): Converts an rxode2 Object Into Specified Model Format

simulate_rules(): Rule-Based simulates

MB Module functions

MB_Server(): Model Builder State Server

MB_append_report(): Append Report Elements

MB_build_code(): Build Code to Generate Model

MB_del_current_element(): Deletes Current model

MB_fetch_appends(): Fetches List of Available Models

MB_fetch_catalog(): Fetches List of Available Models

MB_fetch_code(): Fetch Module Code

MB_fetch_component(): Fetch Selected Current Model Component

MB_fetch_current_element(): Fetches Current model

MB_fetch_mdl(): Fetch Model Builder Module Models

MB_fetch_state(): Fetch Model Builder State

MB_init_state(): Initialize MB Module State

MB_mk_preload(): Make List of Current MB State

MB_new_element(): New Model Building Model

MB_preload(): Preload Data for MB Module

MB_set_current_element(): Sets the Value for the Current model

MB_test_catalog(): Tests the Model Catalog

MB_test_mksession(): Populate Session Data for Module Testing

MB_update_checksum(): Update MB Module Checksum

MB_update_model(): Updates Current Element with rxode2 Model

mk_rx_obj(): Makes an rxode2 Object

NCA Module functions

apply_route_map(): Applies Route Mapping to Dataset

dose_records_builder(): Builds Dose Records Dataframe

flag_nca_ds(): Creates Dataset Flags

mk_table_ind_obs(): Creates Tables of Individual Observations from PKNCA Result

mk_table_ind_obs_flags(): Creates Tables of Manual Flags for Individual Observations from PKNCA Result

mk_table_nca_params(): Create Tabular Output from PKNCA Results

mk_figure_ind_obs(): Creates Figures of Individual Observations from PKNCA Result

NCA_Server(): Fetch Non-Compartmental Analysis State

NCA_add_int(): Adds Analysis Interval to Current Analysis

NCA_append_report(): Append Report Elements

NCA_append_report_old(): Append Report Elements

NCA_fetch_PKNCA_meta(): Fetches PKNCA Metadata

NCA_fetch_ana_ds(): Fetch Analysis Dataset

NCA_fetch_ana_pknca(): Fetch PKNCA Results Object

NCA_fetch_code(): Fetch Module Code

NCA_fetch_current_ana(): Fetches Current Analysis

NCA_fetch_current_obj(): Fetches the Current Analysis Object

NCA_fetch_data_format(): Fetches Details About Data Requirements

NCA_fetch_ds(): Fetch Module Datasets

NCA_fetch_np_meta(): Fetches NCA Parameter Meta Information

NCA_fetch_state(): Fetch ruminate State

NCA_find_col(): Determines Default Column Name

NCA_init_state(): Initialize NCA Module State

NCA_load_scenario(): Loads Pre-Defined Scenario

NCA_mk_preload(): Make List of Current NCA State

NCA_mkactive_ana(): Fetch PKNCA Results Object

NCA_new_ana(): Initialize New Analysis

NCA_preload(): Preload Data for NCA Module

NCA_process_current_ana(): Processes Current Analysis to be Run

NCA_set_current_ana(): Sets Current Analysis

NCA_test_mksession(): Populate Session Data for Module Testing

NCA_update_checksum(): Updates NCA Module Checksum

nca_append_report_figs(): Append NCA Figures to Report

nca_append_report_tbls(): Append NCA Tables to Report

nca_builder(): Builds NCA Code from ui Elements

run_nca_components(): Runs NCA for the Current Analysis